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- PDB-9w2c: Crystal structure of Aedes aegypti Dopachrome Conversion Enzyme w... -

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Basic information

Entry
Database: PDB / ID: 9w2c
TitleCrystal structure of Aedes aegypti Dopachrome Conversion Enzyme with L-Dopamine.
ComponentsDopachrome conversion enzyme
KeywordsISOMERASE / isomerase Dopachrome Aedes aegypti L-Dopamine
Function / homologyMajor royal jelly protein/protein yellow / Major royal jelly protein / Six-bladed beta-propeller, TolB-like / extracellular region / ACETIC ACID / L-DOPAMINE / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Dopachrome conversion enzyme
Function and homology information
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.39 Å
AuthorsGuo, Y. / Zhang, L. / Guo, D. / Li, J. / Deng, J. / Han, Q.
Funding support China, United States, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U22A20363 China
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI044399 United States
CitationJournal: To Be Published
Title: Crystal structure of Aedes aegypti Dopachrome Conversion Enzyme.
Authors: Guo, Y. / Wang, S. / Zhang, L. / Guo, D. / Li, J. / Deng, J. / Han, Q.
History
DepositionJul 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dopachrome conversion enzyme
B: Dopachrome conversion enzyme
C: Dopachrome conversion enzyme
D: Dopachrome conversion enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,03328
Polymers211,7234
Non-polymers5,31024
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13220 Å2
ΔGint-24 kcal/mol
Surface area59610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.308, 103.874, 99.034
Angle α, β, γ (deg.)90.00, 110.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dopachrome conversion enzyme


Mass: 52930.715 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: isomerase/tautomerase / Source: (natural) Aedes aegypti (yellow fever mosquito) / Strain: Liverpool / References: UniProt: Q8T4S2

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Sugars , 8 types, 8 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[LFucpa1-6]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-D-Manp]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4[LFucpa1-6]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-Manp]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-L-arabinopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-3)-[beta-L-arabinopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 985.886 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[LArapb1-6]DManpa1-4DManpb1-3[LFucpa1-6]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a211h-1b_1-5][a1221m-1a_1-5]/1-2-3-2-4-5/a3-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-Manp]{[(4+1)][a-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-L-Arap]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Polysaccharide alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-4DGlcpNAcb1-3[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2-2/a3-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][a-L-Fucp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-Manp]{}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-Manp]{}}LINUCSPDB-CARE
#12: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 44 molecules

#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: Ca
#10: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C2H4O2
#11: Chemical
ChemComp-LDP / L-DOPAMINE / DOPAMINE


Mass: 153.178 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H11NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium cacodylate trihydrate pH 6.5, 0.2 M Calcium acetate hydrate, and 20% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2008
RadiationMonochromator: crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 3.39→30 Å / Num. obs: 23333 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.2
Reflection shellResolution: 3.39→3.52 Å / Rmerge(I) obs: 0.372 / Num. unique obs: 2314

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.39→29.66 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.816 / Cross valid method: THROUGHOUT / ESU R Free: 0.735 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27375 1196 5.1 %RANDOM
Rwork0.19431 ---
obs0.19838 22042 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.02 Å2
2--0.02 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 3.39→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12892 0 343 28 13263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01213667
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612480
X-RAY DIFFRACTIONr_angle_refined_deg0.8631.80518652
X-RAY DIFFRACTIONr_angle_other_deg1.7351.7528768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.98751580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.456585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.643102103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2970.22074
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215944
X-RAY DIFFRACTIONr_gen_planes_other0.0160.023255
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7096.5336349
X-RAY DIFFRACTIONr_mcbond_other4.686.5356334
X-RAY DIFFRACTIONr_mcangle_it7.58311.7357908
X-RAY DIFFRACTIONr_mcangle_other7.58311.7367909
X-RAY DIFFRACTIONr_scbond_it4.937.0587318
X-RAY DIFFRACTIONr_scbond_other4.9297.0587319
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.06112.82210745
X-RAY DIFFRACTIONr_long_range_B_refined11.90865.2514562
X-RAY DIFFRACTIONr_long_range_B_other11.9165.2514563
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.392→3.479 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 87 -
Rwork0.345 1511 -
obs--93.61 %

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